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Detailed information for vg0619058753:

Variant ID: vg0619058753 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19058753
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGAGGGTGGCTTAGGTTCTGTGACGGGTTCTCCAAGATCTTCACTGCTTCTTCTCAGCTGGCTTCACTGCTTCCTCCACTTCGCTAGCGGATCCTGCAG[C/T]
CTTCTGGAGCTTCGGCAGACAATTGACGACATCTTCTTCTTTGCAAAACTAACCATCTAGTACTAGTTGAAATTTGAAGAAGGAAGAAAAGAGTAAACCT

Reverse complement sequence

AGGTTTACTCTTTTCTTCCTTCTTCAAATTTCAACTAGTACTAGATGGTTAGTTTTGCAAAGAAGAAGATGTCGTCAATTGTCTGCCGAAGCTCCAGAAG[G/A]
CTGCAGGATCCGCTAGCGAAGTGGAGGAAGCAGTGAAGCCAGCTGAGAAGAAGCAGTGAAGATCTTGGAGAACCCGTCACAGAACCTAAGCCACCCTCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.60%	21.60%	39.44%	0.44%	NA
All Indica	2759	13.60%	30.70%	55.09%	0.65%	NA
All Japonica	1512	88.40%	4.40%	7.01%	0.13%	NA
Aus	269	9.70%	28.30%	61.71%	0.37%	NA
Indica I	595	8.10%	34.60%	56.64%	0.67%	NA
Indica II	465	7.10%	59.80%	32.69%	0.43%	NA
Indica III	913	21.20%	12.50%	65.28%	0.99%	NA
Indica Intermediate	786	12.60%	31.70%	55.34%	0.38%	NA
Temperate Japonica	767	90.50%	1.30%	8.08%	0.13%	NA
Tropical Japonica	504	86.90%	8.30%	4.56%	0.20%	NA
Japonica Intermediate	241	85.10%	6.20%	8.71%	0.00%	NA
VI/Aromatic	96	49.00%	14.60%	36.46%	0.00%	NA
Intermediate	90	42.20%	16.70%	41.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619058753	C -> T	LOC_Os06g32770.1	upstream_gene_variant ; 329.0bp to feature; MODIFIER	silent_mutation	Average:13.912; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N
vg0619058753	C -> T	LOC_Os06g32780.1	upstream_gene_variant ; 2308.0bp to feature; MODIFIER	silent_mutation	Average:13.912; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N
vg0619058753	C -> T	LOC_Os06g32770-LOC_Os06g32780	intergenic_region ; MODIFIER	silent_mutation	Average:13.912; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N
vg0619058753	C -> DEL	N	N	silent_mutation	Average:13.912; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619058753	5.74E-06	5.97E-08	mr1677	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251